National Innovation System(NIS) is the key to promote innovation capability of a country, and Internet changed ways of storing, obtaining and using knowledge, thereby affecting NIS profoundly. But few literatures analyzed the effect of Internet on NIS empirically. In order to fill up this gap, employing the mothed of grey incidence analysis, this paper investigated the impact of Internet on the whole Chinese NIS as well as main institutions constituted NIS . The empirical result based data of China indicated that: 1) innovation intensity, innovation performance and knowledge transfer have been promoted with Internet development on the whole NIS level; 2)Internet has more influence on innovation performance of research institutes and universities, and more influence on knowledge transfer of firms; 3)the impact of Internet quality are more than Internet penetration. The result of this paper has important theoretical significance to understand the relationship between Internet and NIS, and beneficial enlightenment for policy maker.